From bernd@rs5.thch.uni-bonn.de Fri Jun 20 03:50:12 1997 Received: from IBM.rhrz.uni-bonn.de for bernd@rs5.thch.uni-bonn.de by www.ccl.net (8.8.3/950822.1) id CAA20142; Fri, 20 Jun 1997 02:52:10 -0400 (EDT) Received: from rs5.thch.uni-bonn.de by IBM.rhrz.uni-bonn.de (IBM VM SMTP V2R2) with TCP; Fri, 20 Jun 97 08:51:56 MEZ Received: by rs5.thch.uni-bonn.de (AIX 3.2/UCB 5.64/4.03) id AA17860; Fri, 20 Jun 1997 08:51:48 +0200 From: bernd@rs5.thch.uni-bonn.de (Bernd Engels) Message-Id: <9706200651.AA17860@rs5.thch.uni-bonn.de> Subject: benchmark calculations wanted To: chemistry@www.ccl.net (Computational Chemistry List) Date: Fri, 20 Jun 1997 08:51:47 +0200 (MES) X-Mailer: ELM [version 2.4 PL23] Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit dear ccl'er We developed a new approach for doing individually selected MR-CI calculations. Now we are looking for benchmark calculations so that we can prove the accuracy or/and usefulness of our approach. Any suggestions are highly appreciated. I will summarize. bernd engels From 94970459@vax1.dcu.ie Fri Jun 20 06:50:11 1997 Received: from VAX1.DCU.IE for 94970459@vax1.dcu.ie by www.ccl.net (8.8.3/950822.1) id GAA21027; Fri, 20 Jun 1997 06:39:18 -0400 (EDT) Received: from vax1.dcu.ie by vax1.dcu.ie (PMDF V4.2-12 #4433) id <01IKALMFZTNK8WWD7X@vax1.dcu.ie>; Fri, 20 Jun 1997 11:39:24 GMT Date: Fri, 20 Jun 1997 11:39:24 +0000 (GMT) From: Paddy Kane <94970459@vax1.dcu.ie> Subject: Dihedral Angle Driver To: bisettyk@wpogate.msultan.ac.za Cc: chemistry@www.ccl.net Message-id: <01IKALMG0W8I8WWD7X@vax1.dcu.ie> X-Envelope-to: chemistry@www.ccl.net X-VMS-To: IN%"bisettyk@wpogate.msultan.ac.za" X-VMS-Cc: IN%"chemistry@www.ccl.net" MIME-version: 1.0 Content-transfer-encoding: 7BIT Hi, Please find below the answers that I received in relation to my query about conformational searching in HyperChem. If you wish to write back to me, please do so at my normal address which is: 94970459@tolka.dcu.ie Kind Regards, Paddy. ******************************************************************* The original query was: > > Hi, > > I read that the MM2 force field contains a DIHEDRAL ANGLE DRIVER, which > allows the user to scan part of the potential surface in search of local > minima. > > Can anyone tell me if the MM+ force field which is available in HyperChem > (and which is a variation of the MM2 force field) contains this facility? > If so, how does it compare to other conformational search methods such as > simulated annealing. > > Thanks in advance for your replies. > > Rgds, > Paddy. > > ************************************************************************* > * * > * Paddy Kane email: 94970459@tolka.dcu.ie * > * School of Chemical Sciences * > * Dublin City University Tel: 00-353-1-7045641 * > * Dublin 9 * > * Ireland. Fax: 00-353-1-7045503 * > * * > ************************************************************************* From sopek@hyper.comWed Jun 18 19:39:34 1997 Date: Wed, 9 Apr 1997 19:54:28 -0400 From: dr Miroslaw Sopek To: 'patrick kane' <94970459@tolka.dcu.ie> Subject: RE: Dihedral Angle Driver and HyperChem Hi Patric, Do you have HyperChem 5 ? If so is the case, I have Tcl/Tk 'torsion' utility for E(alpha) analysis. Mirek !-------------------------------------------- ! Mirek Sopek, PhD. ! Senior Project Manager, HyperCube, Inc. ! 1115 NW 4th Street, Gainesville, FL 32601 ! (352)371-7744 fax (352)371-3662 ! sopek@hyper.com, http://www.hyper.com !-------------------------------------------- ! President, MakoLab s.c. ! ul. Piotrkowska 102a ! 90-004 Lodz, Poland ! 011(4842)399716 fax 011(4842)322346 ! sopekmir@mako.com.pl, http://www.mako.com.pl !--------------------------------------------- ******************************************************************* From Tamas@tolka.dcu.ieWed Jun 18 19:40:29 1997 Date: Thu, 10 Apr 1997 11:59:47 +1 From: "tamasgunda@tigris.klte.hu" Reply to: tamasgunda@tigris.klte.hu To: chemistry@www.ccl.net Subject: CCL:Dihedral Angle Driver and HyperChem Not the forcefields itself contain the dihedral driver, but the program & interface, in which the MM procedure has been implanted and realized. In HyperChem there is no dihedral driver, but you can yourself "program" it by creating a script file. Consult the manual of HyperChem. It seems to be difficult only the first time. best wishes Tamas Gunda Dr Tamas E. Gunda phone: (+36-52) 316666 ext 2479 Research Group of Antibiotics fax : (+36-52) 310936 L. Kossuth University e-mail: tamasgunda@tigris.klte.hu POBox 36 H-4010 Debrecen Hungary ******************************************************************* From stavrev@hyper.comWed Jun 18 19:40:43 1997 Date: Thu, 10 Apr 1997 14:29:59 -0400 From: Krassimir Stavrev To: patrick kane <94970459@tolka.dcu.ie> Subject: Re: Dihedral Angle Driver and HyperChem Hi Paddy, Yes, Hyperchem5 contains torsion angle MM+ optimizer that can be used to scan the potential energy surface in a conformational search. If you are already a Hyperchem user, you may wish to check our Reference manual pp.477-483, or the Computational chemistry manual, pp.177-179, and most significantly the torsions description and accuracy of MM+ estimates in the Computational chemistry manual, pp.211-213. Please feel free to contact us, if you would like to have this infor- mation sent to you by FAX. In any case, you can visit our web-page at http://www.hyper.com and have a look at the frequently asked questions under the Support and Questions subdirectories. Regards, Krassimir --- Krassimir Stavrev, PhD Hypercube, Inc. Florida Science and Technology Park 1115 N.W. 4th Street Gainesville, Florida 32601 Voice: 1-352-371-7744/1-800-960-1871 Fax: 1-352-371-3662 From stavrev@hyper.comWed Jun 18 19:41:18 1997 Date: Fri, 11 Apr 1997 12:37:21 -0400 From: Krassimir Stavrev To: patrick kane <94970459@tolka.dcu.ie> Subject: Re: Dihedral Angle Driver and HyperChem patrick kane wrote: > > Hi Krassimir, > > I am presently using HyperChem, version 5. Can you tell me what > facilities are available in that version for scanning the potential > energy surface. > > Can you also tell me how the potential energy scanner in version 5 > compares with techniques such as simulated annealing or the > Conformational Search facility in ChemPlus. > > Rgds, > Paddy. > Hi Paddy, HyperChem 5 has several ways of scaning the potential surfaces as outlined in the Computational Chemistry manual - Single Point, Geometry optimization and Molecular Dynamics. And you can utilize a large variety of approximations to do so - Molecular Mechanics, Semiempirical and Ab initio methods. As far as ChemPlus is concerned it has a special addendum for conformational search which includes: -ring and acyclic systems with no software limitation for the size of the system (see I. Kolossvary et. al, J. Comput. Chem. 14 (1993) 691 for dehedral angle approaches implememnted in ChemPlus) -random variation of dihedral angles with options for choosing initial structure -structural restrictions using MM and Semiemppirical methods, etc. I cannot say know much about comparison with simulated annealing but will try to find some information available and will let you know subsequently. For Conformational search outline in ChemPlus please see: http://www.hyper.com/Descrip/chemplus_features.html#Conformational Search Regards, Krassimir --- Krassimir Stavrev, PhD Hypercube, Inc. Florida Science and Technology Park 1115 N.W. 4th Street Gainesville, Florida 32601 Voice: 1-352-371-7744/1-800-960-1871 Fax: 1-352-371-3662 From Bernard.B.Pirard@GBJHA.zeneca.com Fri Jun 20 12:50:16 1997 Received: from bath.mail.pipex.net for Bernard.B.Pirard@GBJHA.zeneca.com by www.ccl.net (8.8.3/950822.1) id MAA23490; Fri, 20 Jun 1997 12:15:21 -0400 (EDT) X400-Received: by mta bath.mail.pipex.net in /PRMD=pipex/ADMD=pipex/C=gb/; Relayed; Fri, 20 Jun 1997 17:13:26 +0100 X400-Received: by /PRMD=ZENECA/ADMD=PIPEX/C=GB/; Relayed; Fri, 20 Jun 1997 11:49:25 +0100 Date: Fri, 20 Jun 1997 11:49:25 +0100 X400-Originator: Bernard.B.Pirard@GBJHA.zeneca.com X400-Recipients: chemistry@www.ccl.net X400-MTS-Identifier: [/PRMD=ZENECA/ADMD=TMAILUK/C=GB/;970620104925] X400-Content-Type: P2-1984 (2) Content-Identifier: CSI NC V3.0 From: Pirard Bernard B Message-ID: <00168161.MAI*/I=B/G=Bernard/S=Pirard/OU=GBJHA/PRMD=ZENECA/ADMD=PIPEX/C=GB/@MHS> To: cclq Subject: Amber parameters and charges I hope that this message will be readable Dear colleagues, I am currently testing several forcefields for minimization of drug-like molecules. These forcefields are CVFF, CFF91, TRIPOS and AMBER as implemented in SYBYL 6.3. For all the molecules under study, AMBER parameters or charges are missing.So can you tell me whether there is any library of AMBER parameters and charges ? At this point, I can mention that several groups have recently published AMBER parameters for some cofactors. In addition, use of the AMBER forcefield in ligand docking studies has been documented, see for instance the abstracts of the Molecular Graphics Society Meeting held in York (September 1996) but with no details on parameters anc charges. Thanking you in advance for the attention you will pay to this query. I will send a summary of the replies, Sincerely, Bernard Pirard Computational Chemistry Group Zeneca Agrochemicals Jealott s Hill Bernard.B.Pirard@GBJHA.zeneca.com From cornell@cgl.ucsf.EDU Fri Jun 20 14:50:16 1997 Received: from socrates.ucsf.EDU for cornell@cgl.ucsf.EDU by www.ccl.net (8.8.3/950822.1) id OAA24938; Fri, 20 Jun 1997 14:31:12 -0400 (EDT) From: Received: (from cornell@localhost) by socrates.ucsf.EDU (8.8.6/GSC4.26) id LAA14712; Fri, 20 Jun 1997 11:31:08 -0700 (PDT) Date: Fri, 20 Jun 1997 11:31:08 -0700 (PDT) Message-Id: <199706201831.LAA14712@socrates.ucsf.EDU> To: Bernard.B.Pirard@GBJHA.zeneca.com, chemistry@www.ccl.net Subject: Re: CCL:Amber parameters and charges Bernard Pirard of Zeneca inquired about the availability of AMBER parameters for treating generic organic molecules. The primary reference for the "official" AMBER force field is: CORNELL WD; CIEPLAK P; BAYLY CI; GOULD IR; and others. A SECOND GENERATION FORCE FIELD FOR THE SIMULATION OF PROTEINS, NUCLEIC ACIDS, AND ORGANIC MOLECULES. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 1995 MAY 17, V117 N19:5179-5197. The set of parameters described therein represents a complete set for modelling proteins and nucleic acids containing standard residues. The force field is also described as being appropriate for organic molecules, however, the set of parameters available for modelling such molecules is far from complete. When studying the interactions between small molecules and proteins or nucleic acids, bonded parameters can often be borrowed from other force fields. Charges for a new molecule, however, need to be calculated from an ab initio generated HF/6-31G* wave function using the RESP protocol as described in these references: BAYLY CI; CIEPLAK P; CORNELL WD; KOLLMAN PA. A WELL-BEHAVED ELECTROSTATIC POTENTIAL BASED METHOD USING CHARGE RESTRAINTS FOR DERIVING ATOMIC CHARGES - THE RESP MODEL. JOURNAL OF PHYSICAL CHEMISTRY, 1993 OCT 7, V97 N40:10269-10280. CORNELL WD; CIEPLAK P; BAYLY CI; KOLLMAN PA. APPLICATION OF RESP CHARGES TO CALCULATE CONFORMATIONAL ENERGIES, HYDROGEN BOND ENERGIES, AND FREE ENERGIES OF SOLVATION. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 1993 OCT 20, V115 N21:9620-9631. Variations of the AMBER force field have been implemented in various modelling packages and typically include the bonded and VDW parameters but use charges derived using a simpler and less costly approach. These implementations may be quite useful but it should be noted that they differ from the original force field. The "bona fide" AMBER force field was optimized to perform well at calculating relative energies of interaction in solution rather than, for example, screening large sets of compounds in a DOCKing procedure. For those who want to carry out MD studies in solution involving functional groups for which parameters are not available in the JACS reference, members of the Kollman research group as well as other members of the AMBER community often have derived such parameters. We are currently working on developing additional parameters, however, it will still fall to the user to calculate charges for a new molecule. Cheers, =Wendy Cornell _________________________________________________________________________________ Wendy D. Cornell, Ph.D. Senior Scientist Biomolecular Structure and Drug Design Chemistry Parke-Davis Research Ann Arbor, MI 48105 USA From woods@draco.pmmp.uic.edu Fri Jun 20 15:50:18 1997 Received: from draco.pmmp.uic.edu for woods@draco.pmmp.uic.edu by www.ccl.net (8.8.3/950822.1) id PAA25440; Fri, 20 Jun 1997 15:46:18 -0400 (EDT) From: Received: from draco by draco.pmmp.uic.edu via SMTP (940816.SGI.8.6.9/940406.SGI.AUTO) id OAA08274; Fri, 20 Jun 1997 14:50:30 -0500 Sender: woods@draco.pmmp.uic.edu Message-ID: <33AADEF7.2781@mmad1.pmmp.uic.edu> Date: Fri, 20 Jun 1997 14:50:29 -0500 X-Mailer: Mozilla 3.0 (X11; I; IRIX 5.3 IP22) MIME-Version: 1.0 To: Computaional Chemistry List CC: chemistry@www.ccl.net Subject: Re: CCL:Paking in the unit cell References: <9706200411.AA03934@hewl.crystal.uwa.edu.au> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Alexandre N. Sobolev wrote: > > > > > Hi > > Along these same lines, I am seeking a program that will allow > > one to > > build a lattice of molecules by inputting one or several different > > molecular files as well as the unit cell dimensions. I currently > > have a > > routine called bcell that will make a lattice of multiple copies of > > the > > SAME molecule file, but I need a routine that will allow a lattice > > to be > > built which will contain multiple copies of one molecule in the > > lattice, > > as well as ONE that is different. > > > > Anyone have any suggestions? > > > > Richard Hi- Let me clarify what I need as I think there may be a misunderstanding here. I am attempting to build a mono/bilayer of phospholipids for an MD simulation. I wish to have 16/32 copies of the same molecule aligned in space using the unit cell dimensions of a single crystal. What I want to do is selectively introduce a double bond in ONE of the phospholipids. Thus, I want 15/31 saturated lipids and 1 unsaturated lipid. The routine that I have will allow me to assemble multiple copies of ONE file, not two, which is what I need. I used a program called Chemlab to build my original lipid, and i sue it to introduce the unsaturation in my lipid, but I cannot use it to edit a mono/bilayer, as it only handles 999 atoms. I can't modify Chemlab as we don't have access to the code. Any suggestions? Richard From shubin@email.unc.edu Fri Jun 20 16:50:16 1997 Received: from listserv.oit.unc.edu for shubin@email.unc.edu by www.ccl.net (8.8.3/950822.1) id PAA25482; Fri, 20 Jun 1997 15:55:32 -0400 (EDT) Received: from login1.isis.unc.edu ([152.2.25.131]) by listserv.oit.unc.edu with ESMTP id <222499-4072>; Fri, 20 Jun 1997 15:41:09 -0400 Received: by email.unc.edu id <15370-5324>; Fri, 20 Jun 1997 15:42:01 -0400 Date: Fri, 20 Jun 1997 15:41:52 -0400 (EDT) Sender: Shubin Liu From: Shubin Liu X-Sender: shubin@login1.isis.unc.edu To: chemistry@www.ccl.net Subject: CCL:Global minimization Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCLers: As geometrical optimization only gives a local minimal, I hope to find a way, if possible, to achieve the global minimal for a molecule. At least, I hope that some way to check if the optimized structure is a local or global minimal is available somewhere. Any comments are welcome. Thanx. Shubin ............................................................................. Shubin Liu Department of Chemistry Email: shubin@email.unc.edu Kenan Hall A207, CB# 3290 sliu@mulliken.chem.unc.edu University of North Carolina Home Page: http://www.unc.edu/~shubin Chapel Hill, NC 27599-3290 Tel : (919) 962-0150 (Office) USA Fax : (919) 962-2388 ............................................................................. From harvey@www.chem.tu-berlin.de Thu Jun 19 05:50:05 1997 Received: from www.chem.TU-Berlin.DE for harvey@www.chem.tu-berlin.de by www.ccl.net (8.8.3/950822.1) id FAA08636; Thu, 19 Jun 1997 05:24:15 -0400 (EDT) Received: from ioc4-11 (unverified [130.149.42.93]) by www.chem.TU-Berlin.DE (EMWAC SMTPRS 0.83) with SMTP id ; Thu, 19 Jun 1997 11:24:15 +0200 Message-Id: <3.0.1.32.19970619112304.0091b8d0@www.chem.tu-berlin.de> X-Sender: harvey@www.chem.tu-berlin.de X-Mailer: Windows Eudora Light Version 3.0.1 (32) Date: Thu, 19 Jun 1997 11:23:04 +0200 To: CHEMISTRY@www.ccl.net From: Jeremy Harvey Subject: CCL:organic synthesis is comp.chem.! In-Reply-To: <26EF0DF487C@virgil.ruc.dk> Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Hello all, I used to do some organic synthesis, and before starting a reaction, I would try to work out how much reagent I needed from the mol. weights, stoechiometry, etc. To do this, I often used a ... pocket calculator ! So organic synthesis is right at the heart of computational chemistry ! More seriously, I doubt whether a definition is upcoming or even desirable. J. E. Huheey gives a nice definition of Inorganic Chemistry in his text book : "Inorganic Chemistry is any phase of chemistry of interest to an inorganic chemist." I don't think we'll do any better when attempting to define Comp. Chem. or Molecular Modelling. But that won't stop us doing/enjoying it ! Best regards, Jeremy __________________________________ Dr. Jeremy N. Harvey Technische Universitaet Berlin Institut fur Organische Chemie Sekretariat C4 Strasse des 17. Juni, 135 D-10623 BERLIN Tel. (49) 030 314 26546 Fax. (49) 030 314 21102 harvey@www.chem.tu-berlin.de __________________________________ From ccl@www.ccl.net Thu Jun 19 06:49:58 1997 Received: from bedrock.ccl.net for ccl@www.ccl.net by www.ccl.net (8.8.3/950822.1) id GAA08950; Thu, 19 Jun 1997 06:31:06 -0400 (EDT) Received: from pp2.shef.ac.uk for D.J.Wild@sheffield.ac.uk by bedrock.ccl.net (8.8.3/950822.1) id GAA11526; Thu, 19 Jun 1997 06:31:02 -0400 (EDT) Received: from ramsley.shef.ac.uk by pp2.shef.ac.uk with local SMTP (PP); Thu, 19 Jun 1997 11:30:23 +0100 Received: from RAMSLEY/MAILQUEUE by ramsley.shef.ac.uk (Mercury 1.21); 19 Jun 97 11:30:25 +0100 Received: from MAILQUEUE by RAMSLEY (Mercury 1.30); 19 Jun 97 11:30:07 +0100 From: David Wild To: ooms@scf.fundp.ac.be (ooms fred) Date: Thu, 19 Jun 1997 11:30:06 +0100 Subject: Re: CCL:MEP similarity Reply-to: D.J.Wild@sheffield.ac.uk CC: chemistry@ccl.net X-Confirm-Reading-To: D.J.Wild@sheffield.ac.uk X-pmrqc: 1 Priority: normal X-mailer: Pegasus Mail for Windows (v2.42a) Message-ID: <8F9F2363B0@ramsley.shef.ac.uk> Fred Oooms (ooms@scf.fundp.ac.be) wrote: > Dear netters > I would like to compare similarities between MEP of different > molecules and also to compare the MEP obtained by different methods > for the same compound. Which are the similarity index to be used to > do this kind of job. Any assistance would be appreciated. Thanks > Fred The usual way (but not by any means only way) of doing this is to use something like the Carbo Index: ( integral (PaPb) dv) / ( integral(Pa*Pa)dv**0.5 * integral(Pb*Pb)dv**0.5) or the Hodgkin Index: (2*integral (Pa*Pb)dv) / (integral(Pa*Pa)dv + integral (Pb*Pb)dv) Where Pa and Pb are the MEP functions for the molecules a and b resprectively. These integrate the MEP over volume to create a field, and effectively calculate the overlap between the fields of the two molecules to produce a single similarity measure. Good & Richards describe a way of quickly evaluating this integral using Gaussian approximations. Calculating the overlap requires that the molecules are first aligned so their fields overlay optimally. This may be done manually or automatically - a vairety of programs are available to do this. We have developed one called FBSS which can align molecules and calculate MEP (and now also shape and hydrophobic) similarity between them. Useful papers to read are Good, A.C., J. Mol. Graphics, 1992, Vol 10, 144-151 (similarity measures), Good, A.C., Richards, W.G., J. Chem. Inf. Comput. Sci, 1993, 33, 112-116 (gaussian method), Wild, D.J., Willett, P., J. Chem. Inf. Comput. Sci 1996, 36, 159-167 and Thorner, D.A., Wild, D.J, Willett, P., Wright, P.M., J. Chem. Inf. Comput. Sci., 1996, 36, 900-908 (FBSS) Hope this is of some use! David __________________________________________________ Dr. David Wild, Computational Chemistry Group, Department of Information Studies, University of Sheffield, Sheffield S10 2TN, U.K. Tel +44-(0)114 22 22669, Fax +44-(0)114 278 0300 Email D.J.Wild@sheffield.ac.uk http://www.shef.ac.uk/uni/academic/I-M/is/research/cisrg/davewild.html From morokuma@euch4e.chem.emory.edu Thu Jun 19 13:49:59 1997 Received: from euch4e.chem.emory.edu for morokuma@euch4e.chem.emory.edu by www.ccl.net (8.8.3/950822.1) id NAA13235; Thu, 19 Jun 1997 13:00:12 -0400 (EDT) From: Received: by euch4e.chem.emory.edu (AIX 3.2/UCB 5.64/4.03) id AA19114; Thu, 19 Jun 1997 13:00:13 -0400 Message-Id: <9706191700.AA19114@euch4e.chem.emory.edu> Subject: 9th ICQC To: chemistry@www.ccl.net Date: Thu, 19 Jun 1997 13:00:12 -0400 (EDT) X-Mailer: ELM [version 2.5 PL0b1] Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit The Book of Abstract the 9th International Congress of Quantum Chemistry June 9-14, 1997, Emory University, Atlanta, GA, USA is now available at cost. The cost (including shipping and handling) is $30 for US and Canada, and $40 for all other countries via ISAL. It contains the abstracts of 80 plenary and invited lectures and 373 contributed papers. Send a check in US dollars, written to the 9th ICQC, Emory University and payable at a US bank, or send credit card information (card number, expiration date, the name of the card owner, the authorized amount, signature) to the address below. 9th ICQC '97 Department of Chemistry Emory University Atlanta, GA 30322 USA Phone: (404) 727-0867 Fax: (404) 727-6586 Email: icqc@euch4g.chem.emory.edu ______________________ Keiji Morokuma Emerson Center for Scientific Computation and Department of Chemistry Emory University Atwood Hall, 1515 Pierce Dr., Atlanta, GA 30322, USA Phone (404) 727-2180; Fax (404) 727-6586 E-mail: morokuma@emory.edu From bartberg@chem.ufl.edu Fri Jun 20 02:50:12 1997 Received: from mailey for bartberg@chem.ufl.edu by www.ccl.net (8.8.3/950822.1) id CAA19340; Fri, 20 Jun 1997 02:00:13 -0400 (EDT) Received: from localhost by mailey (SMI-8.6/4.11) id AAA14330; Fri, 20 Jun 1997 00:59:39 -0500 Date: Fri, 20 Jun 1997 01:59:39 -0400 (EDT) From: "Michael D. Bartberger" X-Sender: bartberg@mailey Reply-To: "Michael D. Bartberger" To: Computational Chemistry List Subject: BSSE in cyclophanes? Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Greetings: I am currently investigating the thermodynamics of formation for a series of substituted para-cyclophanes, of the general type CH2---Ph---CH2 | | | | CH2---Ph---CH2 /CH=CH\ as formed from their xylylene "monomers": 2 CH2=C C=CH2 \CH=CH/ (pardon the ASCII artwork!) Methodology so far has been as follows: geometry optimizations and frequencies/ZPE determination at RHF/3-21G (I'd like to go larger but I have other substituted systems where the number of heavy atoms gets quite large) with single-point energies at MP2/6-31G* and B3LYP/6-31G* on the RHF/3-21G geometries. I've been worrying about BSSE. As far as I've determined from following various threads of discussion on this list, BSSE manifests itself when determining energetics of interacting vs. isolated "monomers", where a superposition of molecule A's basis functions onto molecule B (and vice versa) occurs. I can see the ramifications of this, in, say, a case such as the acetic acid dimer, for instance. Where I'm unsure is when the "dimer" is formally bound, such as above. Should one account for BSSE effects in such a case? Surely some superposition of basis functions onto adjacent/nearby nuclei occurs (?)- if so, then it most certainly does so in just about any other organic system (again, ??) :) Pardon me, I don't mean to get too philosophical.......and I hope the question is not ridiculous. The burning question is the following: where does one draw the line when deciding to incorporate BSSE effects? Intuitively, I'd imagine one does not include them in a case like this, a formally it (the dimer) is a single molecule........ otherwise, BSSE would become a factor in, for example, [4+2] or other cycloadditions, or for that matter, any other reaction where bonds are being formed. Am I thinking too hard about this???? :) Sorry, it's late..... I'll certainly summarize responses- I'd greatly appreciate any insight the community might be able to lend. Thanks very much! Best Regards, -Michael ________________________________________________________________________________ Michael D. Bartberger bartberg@chem.ufl.edu TEL: (352) 392-3580 Department of Chemistry bartberg@qtp.ufl.edu FAX: (352) 846-0296 University of Florida Gainesville, FL 32611 USA ________________________________________________________________________________ From toukie@zui.unizh.ch Fri Jun 20 04:04:01 1997 Received: from zzmkgtw.zzmk.unizh.ch for toukie@zui.unizh.ch by www.ccl.net (8.8.3/950822.1) id CAA20149; Fri, 20 Jun 1997 02:53:44 -0400 (EDT) Received: by zzmkgtw.zzmk.unizh.ch; (5.65v3.2/1.3/10May95) id AA07645; Fri, 20 Jun 1997 08:53:17 +0200 Message-Id: <1.5.4.32.19970620065528.0067dd04@highdent.zzmk.unizh.ch> X-Sender: toukie@highdent.zzmk.unizh.ch (Unverified) X-Mailer: Windows Eudora Light Version 1.5.4 (32) Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Fri, 20 Jun 1997 08:55:28 +0200 To: chemistry@www.ccl.net From: "Hr. Dr. S. Shapiro" Subject: MOPAC7 Cc: toukie@zui.unizh.ch Dear Colleagues; I'm sure that we've all heard the dire warnings from Dr. J. Stewart re applying MOPAC7 to experimental work. In view of these warnings, I'd be grateful to hear from persons who have had an opportunity to compare "challenging" calculations using both MOPAC7 and one of the versions of MOPAC93 and are willing to share their experiences and opinions with me. I'd also like to know if anyone knows of any _published_ references to experimental work performed using MOPAC7. If so, kindly send me the citations. Thanks in advance to all responders. Sincerely, S. Shapiro toukie@zui.unizh.ch From lestaw.k.bieniasz@uni-tuebingen.de Fri Jun 20 04:04:12 1997 Received: from outmail.zdv.uni-tuebingen.de for lestaw.k.bieniasz@uni-tuebingen.de by www.ccl.net (8.8.3/950822.1) id DAA20349; Fri, 20 Jun 1997 03:36:09 -0400 (EDT) Received: from echem5.orgchemie.chemie (echem5.orgchemie.chemie.uni-tuebingen.de) by outmail.zdv.uni-tuebingen.de (4.1/ZDV-Uni-Tuebingen-1.0) id AA16595; Fri, 20 Jun 97 09:36:03 MES Date: Fri, 20 Jun 1997 09:35:11 +0200 (W. Europe Daylight Time) From: "Lestaw K. Bieniasz" To: chemistry@www.ccl.net Subject: CC semantics Message-Id: X-X-Sender: coibi01@mailserv.uni-tuebingen.de Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Tuebingen, 20.06.97 Dear Drs. Buyong Ma and Prem Yadav, I wonder how you would classify the following types of evidently chemical and computational research: 1) computer modelling of combustion phenomena (hundreds of species and reactions, highly nonlinear systems of ODEs or PDEs, intractable by analytical approaches), 2) computer modelling of spatio-temporal nonlinear dynamic effects in chemical reaction-diffusion systems by cellular automata methods, 3) computer modelling of electrochemical microelectrode assemblies in two or three-dimensional geometry (complex PDE systems with sophisticated boundary conditions, over non-trivial space domains. 4) investigations of the chemical inference rules for automating analytical chemistry measurement systems, and their practical implementation in the form of expert systems. None of these examples is molecular modelling, but I daresay all of them are computational chemistry. Sincerely, L.Bieniasz *-------------------------------------------------------------------* | Dr. Leslaw Bieniasz | | temporary address: (3rd April 1997 - 31st August 1997) | | Institut fuer Organische Chemie, Universitaet Tuebingen | | Auf der Morgenstelle 18, 72076 Tuebingen, Germany. | | E-mail: lestaw.k.bieniasz@uni-tuebingen.de | *-------------------------------------------------------------------* | permanent address: | | Institute of Physical Chemistry of the Polish Academy of Sciences,| | Molten Salts Laboratory, ul. Zagrody 13, 30-318 Cracow, Poland. | | E-mail: nbbienia@cyf-kr.edu.pl | *-------------------------------------------------------------------* From mzloh@ulsop.ac.uk Fri Jun 20 10:50:14 1997 Received: from chemb.pharm.lon.ac.uk for mzloh@ulsop.ac.uk by www.ccl.net (8.8.3/950822.1) id KAA22383; Fri, 20 Jun 1997 10:20:13 -0400 (EDT) Received: from localhost (mzloh@localhost) by chemb.pharm.lon.ac.uk (8.6.9/8.6.9) with SMTP id PAA17319 for ; Fri, 20 Jun 1997 15:24:22 GMT X-Authentication-Warning: chemb.pharm.lon.ac.uk: mzloh owned process doing -bs Date: Fri, 20 Jun 1997 15:24:21 +0000 (GMT) From: Mire Zloh X-Sender: mzloh@chemb To: CHEMISTRY@www.ccl.net Subject: Help with X-PLOR Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, I have tried recently to do molecular dynamics with saving the trajectory. I am getting the following error message: %WRITEV-ERR: invalid logical unit on three different versions of X-PLOR, under the LINUX and SUN OS operating systems. I have been using the following dynamics statement. dynamics verlet trajectory=loop23_sol.dcd nsavv=10 nstep=$steps timestep=0.001 iasvel=maxwell firstt=$init_t tcoupling=true tbath=$init_t nprint=25 iprfrq=0 rbuf=27 end All other protocols (DG, SA) are working fine. Please, could anybody point the mistake(s) I am making? Yours, ========================================================== Mr Mire Zloh | School of Pharmacy | e-mail: mzloh@ulsop.ac.uk 29 Brunswick Square | Tel: + 44 171 753 5804 London WC1N 1AX | Fax: + 44 171 278 1939 ========================================================== "There are many paths leading to the top of Mount Fuji, but there is only one summit ..." "The Art of Peace" by Morihei Ueshiba ==========================================================